AMBER Archive (2006)

Subject: AMBER: pdb error

From: AYTUG TUNCEL (ATUNCEL_at_ku.edu.tr)
Date: Tue Aug 01 2006 - 14:36:39 CDT

hi all,

I am trying to use MM-PBSA method to calculate free energies for my system. the problem is that I have simulated my system using NAMD and now ı have to convert .dcd (NAMD trajectory file) and .pdb (prepared with VMD) to AMBER formats. I guess I have handled the trajectory formats but I also need .prmtop file for my system. When I try to prepare it using LeAP it gives the error;

"unknown residue: TIP number xxx type: Nonterminal"

Is there any way to convert VMD prepared PDB format to the AMBER format so that LeAP can recognize it.

Thanks for any help.

Aytug TuncelÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿR

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